Changeset 972

Timestamp:

Nov 15, 2016, 5:22:14 PM (8 years ago)

Author:

sommeria

Message:

multitif updated

Location:

trunk/src

Files:

• mouse_motion.m (modified) (1 diff)
• phys_XYZ.m (modified) (1 diff)
• phys_ima.m (modified) (1 diff)
• series.m (modified) (3 diffs)
• series/extract_multitif.m (modified) (5 diffs)
• series/extract_multitif_parallel.m (added)
• transform_field/ima_color2BW.m (modified) (1 diff)
• uvmat.m (modified) (3 diffs)

trunk/src/mouse_motion.m

@@ -224 +224 @@
                     sin_om=sin(pi*om/180);
                     pos=[xy(1,1) xy(1,2) 0];
-                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
-                end
-               pos=pos+Field.ProjObjectCoord;
+                    %pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
+                    coeff=OmAxis(3)*(1-cos_om);
+                    norm_plane(1)=OmAxis(1)*coeff+OmAxis(2)*sin_om;
+                    norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om;
+                    norm_plane(3)=OmAxis(3)*coeff+cos_om;
+                    %Z0=norm_plane*Field.ProjObjectCoord'/norm_plane(3);
+                    pos(3)=-(norm_plane(1)*pos(1)-norm_plane(2)*pos(2))/norm_plane(3);                               
+                end
+                pos=pos+Field.ProjObjectCoord;
                 text_displ_3=[text_displ_3 'x,y,z=' num2str(pos,4)];
             end

trunk/src/phys_XYZ.m

@@ -41 +41 @@
         norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om;
         norm_plane(3)=OmAxis(3)*coeff+cos_om;
-        Z0=norm_plane*Calib.SliceCoord(Zindex,:)'/norm_plane(3);
-    else
+%         Z0=norm_plane*Calib.SliceCoord(Zindex,:)'/norm_plane(3);
+    end
         Z0=Calib.SliceCoord(Zindex,3);%horizontal plane z=cte
-    end
+%     end
     Z0virt=Z0;
     if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex')

trunk/src/phys_ima.m

@@ -61 +61 @@
         [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
         [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
-    else         
+    else
         % the image needs to be interpolated to the new coordinates
         zphys=0; %default
         if isfield(Calib,'SliceCoord') %.Z= index of plane
-           SliceCoord=Calib.SliceCoord(ZIndex,:);
-           zphys=SliceCoord(3); %to generalize for non-parallel planes
-           
-%         if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
-%                     om=norm(Calib.SliceAngle);%norm of rotation angle in radians
-%                     OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
-%                     cos_om=cos(pi*om/180);
-%                     sin_om=sin(pi*om/180);
-%                     pos=[xy(1,1) xy(1,2) 0];
-%                     pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
-%                 end
-           
-           
-%            if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') 
+            SliceCoord=Calib.SliceCoord(ZIndex,:);
+            zphys=SliceCoord(3); %to generalize for non-parallel planes
+            if isfield(Calib, 'SliceAngle') && ~isequal(Calib.SliceAngle,[0 0 0]) && ~isequal(Calib.SliceAngle(ZIndex,:),[0 0 0])
+                testangle=1;
+                om=norm(Calib.SliceAngle(ZIndex,:));%norm of rotation angle in radians
+                OmAxis=Calib.SliceAngle(ZIndex,:)/om; %unit vector marking the rotation axis
+                cos_om=cos(pi*om/180);
+                sin_om=sin(pi*om/180);
+                coeff=OmAxis(3)*(1-cos_om);
+                norm_plane(1)=OmAxis(1)*coeff+OmAxis(2)*sin_om;
+                norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om;
+                norm_plane(3)=OmAxis(3)*coeff+cos_om;
+                %Z0=norm_plane*Calib.SliceCoord(ZIndex,:)'/norm_plane(3);
+                Z0=Calib.SliceCoord(ZIndex,3);
+                zphys=Z0-(norm_plane(1)*X-norm_plane(2)*Y)/norm_plane(3);
+            end
+%             if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex')
 %                 H=Calib.InterfaceCoord(3);
 %                 if H>zphys
 %                     zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object)
 %                 end
-%            end
+%             end
         end
         xima=0.5:npx(icell)-0.5;%image coordinates of corners

trunk/src/series.m

@@ -2714 +2714 @@
 end
 
+
 function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
 [i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
@@ -3486 +3487 @@
 
 % --- Executes on button press in SetPairs.
-function SetPairs_Callback(hObject, iview, handles)
+function SetPairs_Callback(hObject, eventdata, handles)
 
 %% delete previous occurrence of 'set_pairs'
@@ -3510 +3511 @@
 ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
 ListViewMenu=cell(numel(ListViewLines),1);
+iview=get(handles.PairString,'Value');
 for ilist=1:numel(ListViewLines)
     ListViewMenu{ilist}=num2str(ListViewLines(ilist));

trunk/src/series/extract_multitif.m

@@ -59 +59 @@
 %=======================================================================
 
-function ParamOut=ima2netcdf(Param)
+function ParamOut=extract_multitif(Param)
 
 %%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
@@ -73 +73 @@
     ParamOut.OutputDirExt='.png';%set the output dir extension
     ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
-    
+     ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
     %% root input file(s) and type
     % check the existence of the first file in the series
@@ -148 +148 @@
 %count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1
 %count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images
-%% loop on the files 
+%% loop on the files  
 for ifile=1:numel(ListFile)
     update_waitbar(WaitbarHandle,ifile/numel(ListFile))
@@ -158 +158 @@
     NbFrames=numel(imfinfo(ImageName));
     % loop on the frames within the tiff file
-    for iframe=1:NbFrames      
-        A=imread(ImageName,iframe);
-
-        if isequal(ImagesPerLevel,1)% mode series 
+    for iframe=1:NbFrames       
+        if isequal(ImagesPerLevel,1)% mode series
             i_index=count+1;
             OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']);
-        else % indices i and j 
+        else % indices i and j
             i_index=fix(count/ImagesPerLevel)+1;
             j_index=mod(count,ImagesPerLevel)+1;
             OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
         end
-        imwrite(A,OutputFile,'BitDepth',16)
+        if Param.CheckOverwrite ||~exist(OutputFile,'file')
+            A=imread(ImageName,iframe);
+            imwrite(A,OutputFile,'BitDepth',16);
+            disp([OutputFile ' written'])
+        else
+            disp([OutputFile ' already exists'])
+        end
         count=count+1;
     end
 end
+
+% for ifile=1:numel(ListFile)
+%     update_waitbar(WaitbarHandle,ifile/numel(ListFile))
+%     if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
+%         disp('program stopped by user')
+%         break
+%     end
+%     ImageName=fullfile(DirImages,ListFile{ifile});
+%     NbFrames=numel(imfinfo(ImageName));
+%     % loop on the frames within the tiff file
+%     for iframe=1:NbFrames      
+%         A=imread(ImageName,iframe);
+% 
+%         if isequal(ImagesPerLevel,1)% mode series 
+%             i_index=count+1;
+%             OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']);
+%         else % indices i and j 
+%             i_index=fix(count/ImagesPerLevel)+1;
+%             j_index=mod(count,ImagesPerLevel)+1;
+%             OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
+%         end
+%         imwrite(A,OutputFile,'BitDepth',16)
+%         count=count+1;
+%     end
+% end
 
 %% create the xml file of PCO camera
@@ -181 +210 @@
 
 %% remove initial files if transfer OK
-    if i_index== (size(XmlInput.Time,1)-1)
-
-        [SUCCESS,MESSAGE]=rmdir(DirImages,'s')
-       
-    end
+%     if i_index== (size(XmlInput.Time,1)-1)
+% 
+%         [SUCCESS,MESSAGE]=rmdir(DirImages,'s')
+%        
+%     end

trunk/src/transform_field/ima_color2BW.m

@@ -30 +30 @@
 DataOut=DataIn; %default
 if ndims(DataOut.A)==3
-    DataOut.A=uint16(sum(double(DataOut.A,3)));%sum on color components, transform in 16 bit BW images
+    DataOut.A=uint16(sum(double(DataOut.A),3));%sum on color components, transform in 16 bit BW images
 end
  

trunk/src/uvmat.m

@@ -1177 +1177 @@
     'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_1'':first slice angle of inclination around the x axis');%edit box
 uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_2','BackgroundColor',[1 1 1],...
-    'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination around the x axis');%edit box
+    'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination around the x axis');%edit box
 uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_1','BackgroundColor',[1 1 1],...
-    'String',num2str(SliceAngle(1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination around the y axis');%edit box
+    'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination around the y axis');%edit box
 uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_2','BackgroundColor',[1 1 1],...
     'String',num2str(SliceAngle(2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_2'':last slice angle of inclination around the y axis');%edit box
@@ -1269 +1269 @@
 uvmat('InputFileREFRESH_Callback',huvmat,[],hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
 set(hObject,'BackgroundColor',[1 0 0]);% paint button back to red
+
+delete(hset_slice)
 
 %------------------------------------------------------------------------
@@ -1338 +1340 @@
 function set_slice_Cancel_Callback(hObject,eventdata)
 %------------------------------------------------------------------------
-hfig=get(hObject,'parent');
-delete(hfig)
+hset_slice=get(hObject,'parent');
+delete(hset_slice)
 
 %-----------------------------------------------------------------------